Integration of physical and linkage maps is a critical step in building necessary genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole genome assembly. Previously, we have established both linkage maps and a physical map for channel catfish,

Ictalurus punctatus, the dominant aquaculture species in the U.S. Here we added 2,030 BAC-end sequence-derived microsatellites from 1,481 physical map contigs to a high-density linkage map also containing singleton BES, EST, and anonymous microsatellite markers as well as SNPs. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. Several hundred physical map contigs were anchored to the linkage group with two or more BES markers, providing a reasonably accurate basis for determination of ratios of physical to genetic map distances. These ratios ranged from 4 kb/cM to 4,830 kb/cM with an average of 455 kb/cM. The work effectively anchored close to 50% of the catfish BAC physical map contigs (~51% of the genome) to genetic linkage groups enabling future comparative studies with teleost model species as well as providing a framework for ordering and assembly of whole genome scaffolds.